Myopia is a common eye problem worldwide and is more prevalent in Oriental than in Caucasian populations. Subjects with high myopia are vulnerable to ocular complications later in life. The present study aimed to test linkage and association between high myopia and three candidate genes (MYOC, MMP2 and COL2A1) of myopia susceptibility by family-based association study approach. First, family-based association tests were performed on the COL2A1, MYOC and MMP2 genes in Han Chinese families in Hong Kong. All these genes are expressed in eyes and were selected based on their putative biological functions related to myopia. The COL2A1 gene is located at chromosome 12ql3.11-ql3.2 and encodes collagen type 2 alpha 1. Mutations in COL2A1 account for Sticker syndrome type I (STL1). Myopia is a common clinical feature of STL1. The myocilin gene (MYOC) is located at chromosome Iq24.3-q25.2 and encodes the myocilin protein. The MYOC polymorphisms were found associated with primary open angle glaucoma. Previous studies provided inconclusive evidence of association between the MYOC microsatellites (NGA17 and NGA19) and myopia in the Chinese population of Singapore. The MMP2 gene is at chromosome 16ql3-q21 and encodes matrix metalloproteinase-2 enzyme, which breaks down extracellular matrix of sclera during myopia development. In total, 219 nuclear families (869 individuals) were included. Each family consisted of both parents and at least one high myopic offspring with &lt;=-5.00D of spherical power for both eyes. A comprehensive eye examination and venous blood collection were carried out for each subject. DNA was extracted from the blood sample and used for individual genotyping of genetic markers in the candidate genes. Family-based association analysis was performed for testing linkage/association between the candidate gene polymorphisms and high myopia. The results showed no definitive linkage/association of both COL2A1 and MMP2 genes with susceptibility to high myopia. Only significant linkage/association was shown between the polymorphisms (NGA17, NGA19, rs2421853 and rs235858) in the 3' flanking region of the MYOC gene and high myopia under one to three genetic models (additive, dominant and recessive models) even after correction of multiple comparisons by false discovery rate. Positive linkage and association of the two SNPs with high myopia is a novel finding, the evidence is particularly impressive for rs235858 (p=4.0x10-6 under an additive genetic model, and p=2.5x10-5 under dominant/recessive genetic models). Second, an exploratory study was conducted to assess the technical performance of TaqMan genotyping assay for estimating SNP allele frequency in DNA pools. MYOC SNPs were investigated by this method in two DNA pools conveniently constructed from the parents and the myopic siblings. Preliminary results showed that this real-time PCR technique was rapid and gave reproducible estimates of relative allele frequencies, but its accuracy remains to be proved. In conclusion, MYOC was found associated with high myopia. The polymorphisms in the 3' flanking region of the MYOC gene are potential candidates of altering the risk for myopia and are worthy of further replication and functional study. The TaqMan method requires further studies before being used for estimating allele frequencies in DNA pools on a large scale.